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Graph Database Fundamental Services Bachelor Project Czech Technical University in Prague Faculty of Electrical Engineering F3 Department of Cybernetics Graph Database Fundamental Services Tomáš Roun Supervisor: RNDr. Marko Genyk-Berezovskyj Field of study: Open Informatics Subfield: Computer and Informatic Science May 2018 ii Acknowledgements Declaration I would like to thank my advisor RNDr. I declare that the presented work was de- Marko Genyk-Berezovskyj for his guid- veloped independently and that I have ance and advice. I would also like to thank listed all sources of information used Sergej Kurbanov and Herbert Ullrich for within it in accordance with the methodi- their help and contributions to the project. cal instructions for observing the ethical Special thanks go to my family for their principles in the preparation of university never-ending support. theses. Prague, date ............................ ........................................... signature iii Abstract Abstrakt The goal of this thesis is to provide an Cílem této práce je vyvinout webovou easy-to-use web service offering a database službu nabízející databázi neorientova- of undirected graphs that can be searched ných grafů, kterou bude možno efektivně based on the graph properties. In addi- prohledávat na základě vlastností grafů. tion, it should also allow to compute prop- Tato služba zároveň umožní vypočítávat erties of user-supplied graphs with the grafové vlastnosti pro grafy zadané uži- help graph libraries and generate graph vatelem s pomocí grafových knihoven a images. Last but not least, we implement zobrazovat obrázky grafů. V neposlední a system that allows bulk adding of new řadě je také cílem navrhnout systém na graphs to the database and computing hromadné přidávání grafů do databáze a their properties. výpočet jejich vlastností. Keywords: Node.js, Wolfram Klíčová slova: Node.js, Wolfram Mathematica, SageMath, NetworkX, Mathematica, SageMath, NetworkX, Graphviz, PosgreSQL, Graph theory Graphviz, PosgreSQL, Teorie grafů Supervisor: RNDr. Marko Překlad názvu: Základní služby grafové Genyk-Berezovskyj databáze Faculty of Electrical Engineering, Department of Cybernetics, Na Zderaze 269/4, 120 00 Prague 2 iv Contents 1 Introduction 1 6.3.4 Scaling . 36 1.1 Motivation . 1 6.4 SageMath . 37 1.2 Thesis Structure . 2 6.5 Mathematica & NetworkX . 40 2 Features 3 6.6 Speed Comparison . 41 2.1 Searchable database . 3 6.7 Graphviz . 44 2.2 Online Computation . 3 6.8 Database Design . 46 2.3 Graph Visualization . 4 6.8.1 Roles . 46 2.4 Automated Database Maintenance 5 6.8.2 Schema . 47 6.9 Database Administration . 48 3 Technologies & Tools 7 6.9.1 Displaying the current state . 48 3.1 Web Server . 7 6.9.2 Importing New Graphs . 49 3.2 Nginx . 7 6.9.3 Computing Missing Values . 49 3.3 Javascript . 7 6.10 Logging . 50 3.3.1 ES6 . 8 3.3.2 ES7 . 9 7 Testing 51 3.4 Node.js . 10 7.1 Unit Testing . 51 3.4.1 Asynchronous Code Execution 10 7.2 Integration Testing . 52 3.5 Express . 10 7.3 Mocha & Chai . 52 3.6 Webpack . 11 7.4 Code Coverage . 53 3.7 Documentation . 12 7.4.1 Istanbul . 54 3.7.1 JSDoc . 12 7.4.2 Coverage.py . 54 4 Graph6 13 8 Conclusion 55 4.1 Encoding Vertices. 13 8.1 Possible Improvements . 55 4.2 Encoding Edges . 14 A Contents of the included CD 57 4.3 Example . 14 B Bibliography 59 4.4 Possible Problems . 15 C Project Specification 61 5 API Design 17 5.1 /api/image . 17 5.1.1 /api/image/list . 17 5.1.2 /api/image/static . 18 5.1.3 /api/image/gen . 18 5.1.4 Example Requests and Responses . 20 5.2 /api/graph . 20 5.2.1 Simple Query . 20 5.2.2 Advanced Query . 22 5.3 /api/search . 24 6 Implementation 29 6.1 Development & Deployment . 32 6.2 Nginx . 32 6.2.1 Global Configuration . 33 6.2.2 Server Configuration . 33 6.3 Node.js . 34 6.3.1 DB Connection . 35 6.3.2 SQL Injection . 35 6.3.3 Error Handling . 36 v Figures Tables 4.1 Image of a graph represented by 6.1 Speed comparison for selected “Dpw” in graph6. 15 properties. Data shown in seconds. The leftmost column shows the 5.1 Image returned when requesting number of vertices. 43 endpoint from listing 5.2. 19 6.2 Speed comparison of graph instantiation. Data shown in 6.1 The project architecture. 30 seconds. 43 6.2 The project structure at the time of writing. Several files are left out for the sake of brevity. 31 6.3 Server architecture. 37 6.4 Graphs with 60% Edge Density. 45 6.5 Graphs with 80% Edge Density. 45 6.6 Database schema. 47 vi Chapter 1 Introduction This project is a collaboration between several students. My task is to develop the backbone of the application which provides the graph database. This entails, in no particular order, writing a HTTP server that is accessible from the internet and designing an API to communicate with it, maintaining a database containing the graphs themselves, integrating graph libraries that are be used to compute graph properties and deploying the application to a server. Secondary goals include writing a documentation and tests. Sergej Kurbanov’s task is to create a user interface as described in his thesis [21], while Herbert Ullrich investigates the problem of isomorphism as described in his thesis[22]. 1.1 Motivation There are currently only a handful of online services that offer a searchable database of undirected graphs and all of them have limitations which make their use case somehow limited. Services like House of Graphs[8] or Ency- clopedia of Graphs[2] only collect certain classes of graphs or graphs that have been deemed interesting in some way. Our goal is to provide a database of all graphs up to a certain number of vertices regardless of their intrinsic value. We feel that having a complete list of graphs up to a certain number of vertices can prove very valuable to researches. At the same time, certain classes of graphs can be optionally included in the database as well. While there exist searchable graph databases, we are not aware of a general- purpose web service that would allow users to compute properties of user- supplied graphs. Because of the sheer number of non-isomorphic graphs, even on just 11 and 12 vertices (1018997864 and 165091172592), it is impossible to categorize even just a small percentage of graphs and arguably, a lot of interesting graphs have much more vertices. This is a big limitation for most of the graph databases, where users can only search through the very limited list of categorized graphs. The idea of this project is to accept the fact that we will only ever able offer just a tiny portion of all graphs up to a certain size and instead, let users upload their graphs and have our service compute graph properties for them. 1 1. Introduction ..................................... 1.2 Thesis Structure The thesis structure is described below: . Chapter 2 presents an overview of the intended features of the application. Chapter 3 describes the software tools and technologies we decided to use to develop this project as well as a light introduction into the way the tools and technologies interact with each other. Chapter 4 explains the inner workings of the graph6 format that the project relies on heavily. Chapter 5 presents the API design of the web server application. The chapter describes the most important API endpoints as well as the specification, including parameters, status codes and overall behavior. Chapter 6 describes the implementation, the application flow and the way the web server, the database and the graph libraries work together. We also analyze the speed of the graph libraries on selected graph properties. Chapter 7 describes the notion of software testing and code coverage and the way it helps us ensure the correctness of the application. 2 Chapter 2 Features In this chapter we describe the basic features of the project the way they are implemented. 2.1 Searchable database We base the graph service on a model which House of Graphs[8] uses. House of Graphs allows users to query the database based on complex conditions relating to the graph properties. For example, one can search for graphs with a certain number of vertices in conjunction with a certain number of edges. Our goal is to design an API that is expressive enough to encode such complex queries, but which can also be safely translated into SQL. The database should be able store large number of graphs and allow fast lookups. In chapter 5, we describe the API that is used to communicate with the database. In chapter 6, we describe the database schema and the overall design of the database. 2.2 Online Computation As mentioned in chapter 1, there do not exist any web-based services that allow users to upload their own graphs and have the service compute the graph properties. However, there are many graph theory libraries that can be used offline to achieve the same result. Our goal is to select a few of these libraries and integrate them with the web server so that they can be used to compute properties online. We selected three graph libraries for this purpose. Wolfram Mathematica – Mathematica is a technical computing system encompassing a large number of areas of mathematics and numerical computation one of which is a support for many graph theory compu- tations. Mathematica is a commercial closed-source system and uses a proprietary programming language. SageMath – SageMath is a computer algebra system covering many aspects of mathematics including algebra, combinatorics, numerical 3 2.
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